Related papers: A versatile framework for simulating the dynamic m…
Background: Mathematical modeling approaches are becoming ever more established in clinical neuroscience. They provide insight that is key to understand complex interactions of network phenomena, in general, and interactions within the…
We present a generic formulation of the continuum elasticity of an isotropic crosslinked active gel. The gel is described by a two-component model consisting of an elastic network coupled frictionally to a permeating fluid. Activity is…
The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…
The actin cytoskeleton is a semiflexible biopolymer network whose morphology is controlled by a wide range of biochemical and physical factors. Actin is known to undergo a phase transition from a single-filament state to a bundled state by…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
The purpose of this study was to report numerical validation of a 3D finite element model of contracting muscle. The model was based on continuum theory for fibre-reinforced composite materials. Here we simulated contractions for an…
Machine learning has become increasingly popular for efficiently modelling the dynamics of complex physical systems, demonstrating a capability to learn effective models for dynamics which ignore redundant degrees of freedom. Learned…
An approach to the mechanical behaviour of textile composites at the scale of their constituting fibres, using an implicit finite element simulation code, is proposed in this chapter. The approach is based on efficient methods and…
The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles…
The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
Dynamically crosslinked semiflexible biopolymers such as the actin cytoskeleton govern the mechanical behavior of living cells. Semiflexible biopolymers nonlinearly stiffen in response to mechanical loads, whereas the crosslinker dynamics…
We develop a model for gels and entangled solutions of semiflexible biopolymers such as F-actin. Such networks play a crucial structural role in the cytoskeleton of cells. We show that the rheologic properties of these networks can result…
We present a study on filamentous actin solutions containing heavy meromyosin subfragments of myosin II motor molecules. We focus on the viscoelastic phase behavior and internal dynamics of such networks during ATP depletion. Upon…
Actin networks, acting as an engine pushing against an external load, are fundamentally important to cell motility. A measure of the effectiveness of an engine is the velocity the engine is able to produce at a given force, the…
Modeling the behavior of coupled networks is challenging due to their intricate dynamics. For example in neuroscience, it is of critical importance to understand the relationship between the functional neural processes and anatomical…
We characterize the self-assembly of colloidal particles with surface mobile DNA linkers under kinetically limited valence conditions. For this, we put forward a computer simulation model that captures quantitatively the interplay between…
The cooperative action of many molecular motors is essential for dynamic processes such as cell motility and mitosis. This action can be studied by using motility assays in which the motion of cytoskeletal filaments over a surface coated…
Molecular-motor generated active stresses drive the cytoskeleton away from equilibrium, endowing it with tunable mechanical properties that are essential for diverse functions such as cell division and motility[1-5]. Designing analogous…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…